The best guidebooks are Passport's various Regional Guides to Indonesia.  Buy them, borrow them, steal them, as long as you've taken a look before deciding what seems most interesting to you.  Additionally,  the following books may be of interest:

The Malay Archipelago by Alfred Russell Wallace.  Indispensible, but rewards browsing better than a straight read-through.

The Spice Islands Voyage by Tim Severin.  Very readable account of a modern team following in Wallace's wake.  Great for local flavor, includes stops in Sulawesi.

In Search of Conrad by Gavin Young.  May not be available in the U.S.  Enjoyable account of yachties following in Conrad's footsteps.  Want to know about the real Lord Jim?  Read this and find out.

The Scents of Eden  by Charles Corn.  Popular history of the spice trade.  Occasional problems with the writing, but good background.

Shooting the Boh by Tracy Johnston.  The worst-written of the lot.  Potentially interesting account of a potentially disastrous rafting expedition in Kalimantan badly flawed by the writer's amazing self-absorbtion and stupidity.  Despite the high irritation quotient, worthwhile for the parts which concern the trip rather than the author's state of mind.  Read quickly.